Database Commons
Database Commons

a catalog of worldwide biological databases

Database Profile

General information

URL: http://www.nematodegenomes.org
Full name:
Description: 959 Nematode Genomes is a community-curated semantic wiki to coordinate the sequencing efforts of individual labs to collectively sequence 959 genomes spanning the phylum Nematoda.
Year founded: 2012
Last update: NA
Version: v1.0
Accessibility:
Manual:
Accessible
Real time : Checking...
Country/Region: United Kingdom

Classification & Tag

Data type:
DNA
Data object:
Database category:
Major species:
NA
Keywords:

Contact information

University/Institution: University of Edinburgh
Address: Edinburgh EH9 3JT,UK
City: Edinburgh
Province/State:
Country/Region: United Kingdom
Contact name (PI/Team): Sujai Kumar
Contact email (PI/Helpdesk): sujai.kumar@ed.ac.uk

Publications

22058131
959 Nematode Genomes: a semantic wiki for coordinating sequencing projects. [PMID: 22058131]
Kumar S, Schiffer PH, Blaxter M.

Genome sequencing has been democratized by second-generation technologies, and even small labs can sequence metazoan genomes now. In this article, we describe '959 Nematode Genomes'--a community-curated semantic wiki to coordinate the sequencing efforts of individual labs to collectively sequence 959 genomes spanning the phylum Nematoda. The main goal of the wiki is to track sequencing projects that have been proposed, are in progress, or have been completed. Wiki pages for species and strains are linked to pages for people and organizations, using machine- and human-readable metadata that users can query to see the status of their favourite worm. The site is based on the same platform that runs Wikipedia, with semantic extensions that allow the underlying taxonomy and data storage models to be maintained and updated with ease compared with a conventional database-driven web site. The wiki also provides a way to track and share preliminary data if those data are not polished enough to be submitted to the official sequence repositories. In just over a year, this wiki has already fostered new international collaborations and attracted newcomers to the enthusiastic community of nematode genomicists. www.nematodegenomes.org.

Nucleic Acids Res. 2012:40(Database issue) | 27 Citations (from Europe PMC, 2024-05-04)
24058822
Toward 959 nematode genomes. [PMID: 24058822]
Kumar S, Koutsovoulos G, Kaur G, Blaxter M.

The sequencing of the complete genome of the nematode Caenorhabditis elegans was a landmark achievement and ushered in a new era of whole-organism, systems analyses of the biology of this powerful model organism. The success of the C. elegans genome sequencing project also inspired communities working on other organisms to approach genome sequencing of their species. The phylum Nematoda is rich and diverse and of interest to a wide range of research fields from basic biology through ecology and parasitic disease. For all these communities, it is now clear that access to genome scale data will be key to advancing understanding, and in the case of parasites, developing new ways to control or cure diseases. The advent of second-generation sequencing technologies, improvements in computing algorithms and infrastructure and growth in bioinformatics and genomics literacy is making the addition of genome sequencing to the research goals of any nematode research program a less daunting prospect. To inspire, promote and coordinate genomic sequencing across the diversity of the phylum, we have launched a community wiki and the 959 Nematode Genomes initiative (www.nematodegenomes.org/). Just as the deciphering of the developmental lineage of the 959 cells of the adult hermaphrodite C. elegans was the gateway to broad advances in biomedical science, we hope that a nematode phylogeny with (at least) 959 sequenced species will underpin further advances in understanding the origins of parasitism, the dynamics of genomic change and the adaptations that have made Nematoda one of the most successful animal phyla.

Worm. 2012:1(1) | 21 Citations (from Europe PMC, 2024-05-04)

Ranking

All databases:
2088/6000 (65.217%)
Gene genome and annotation:
626/1675 (62.687%)
2088
Total Rank
46
Citations
3.833
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Record metadata

Created on: 2015-06-20
Curated by:
Lin Liu [2022-08-16]
Dong Zou [2018-03-08]
Mengwei Li [2016-03-31]
Mengwei Li [2016-03-24]
Zhang Zhang [2016-01-06]
Mengwei Li [2015-11-21]
Lina Ma [2015-06-30]
Lina Ma [2015-06-27]
Mengwei Li [2015-06-26]